Ontology highlight
ABSTRACT:
PROVIDER: PRJNA838276 | ENA |
REPOSITORIES: ENA
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Project description:The yeast strain Moniliella spathulata SBUG-Y 2180 was isolated from oil-contaminated soil at the Tengiz oil field in the Atyrau region of Kazakhstan on the basis of its unique ability to use crude oil and its components as the sole carbon and energy source. This yeast used a large number of hydrocarbons as substrates (more than 150), including n-alkanes with chain lengths ranging from C10 to C32, monomethyl- and monoethyl-substituted alkanes (C9 – C23), n-alkylcyclo alkanes with alkyl chain lengths from 3 to 24 carbon atoms as well as substituted monoaromatic and diaromatic hydrocarbons. Metabolism of this huge range of hydrocarbon substrates produced a very large number of aliphatic, alicyclic and aromatic acids. 51 of these were identified by GC/MS analyses. This is the first report of the degradation and of the formation of such a large number of compounds by a yeast. Inoculation of barley seeds with M. spathulata SBUG-Y 2180 had a positive effect on shoot and root development of plants grown in oil-contaminated sand, pointing towards potential applications of the yeast in bioremediation of polluted soils.
2021-02-15 | PXD022543 | Pride
Project description:The mycobacterial cell wall is a distinctive thick layer that protects the tubercle bacillus from general antibiotics and the host’s immune system. Mycolic acids, which are long-chain α-alkyl-β-hydroxy fatty acids, are the major constituents of this protective layer, and their synthesis has been shown to be critical for the survival of M. tuberculosis. This model captures the mycolic acid pathway in M. tuberculosis with 197 metabolites participating in 219 reactions catalysed by 28 proteins. The model helps in the rational identification of potential anti-tubercular drug targets.
2024-09-02 | BIOMD0000001046 | BioModels
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
2013-08-24 | GSE50164 | GEO
Project description:The ecophysiology of complete ammonia oxidizing Nitrospira (CMX) and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the relevance of their activity from the ecosystem-level process perspective has remained unclear. We investigated oligotrophic carbonate rock aquifers as a model system to assess the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen. CMX accounted for up to 95% of the ammonia oxidizer communities. Nitrification rates were positively correlated to CMX clade A-associated phylotypes and AOB affiliated with Nitrosomonas ureae. Surprisingly, short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed more than 90% to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOA and AOB was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater is primarily governed by AOB. Higher growth yields at lower NH4+ turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations. Activity measurements combined with differential inhibition allowed a refined understanding of ammonia oxidizer coexistence, competition and cooperation beyond the insights from molecular data alone.
2023-10-24 | PXD039573 | Pride
Project description:P. aeruginosa is the leading cause of death in patients with cystic fibrosis patients and one of the most problematic bacterial pathogens responsible for hospital-acquired infections. This pathogen has a high capacity to form biofilms on inert and living surfaces. This lifestyle allows it to persist in various hospital niches or on medical device which become vectors of contamination. Chronic infections are extremely complicated to eradicate due to the remarkable antimicrobial resistance of biofilms leading to a persistence in the tissue and an immune system exhaustion. It is therefore becoming essential to understand the mechanisms of biofilm formation to find new therapeutic targets in order to develop effective antibiofilm strategies. We previously identified in P. aeruginosa PA01 biofilms an accumulation of a hypothetical protein named PA3731 and its deletion impacted the biofilm formation. Similarly, to PspA, a protein from the well-known Psp system of E. coli, PA3731 is a has a predicted structure mostly helical, a PspA/IM30 domain and was accumulated during an osmotic shock. In P. aeruginosa genome, PA3731 appears to form a cluster with 3 genes (PA3732 to PA3729) that we named BAC system for “Biofilm Associated Cluster”. Here we worked on the PA14 strain and focus our study on PA14_16140, the PA3732 homologue. Using a ∆16140 mutant and phenotypic approach, we confirmed the role of the BAC system in the virulence and biofilm formation. We added supplementary genes coding the BAC system and demonstrate that altogether they form an operonic structure regulates by RpoN. We get further insight the role PA14_16140 by proteomic quantitative approach revealing an accumulation of the BAC system proteins in ∆16140 biofilms suggesting its regulatory role of the bac operon. Moreover, we present here the first crystallographic structure of PA14_16140. To summarise, according to our studies, and although further analysis is still required, this newly discovered operon appears composed firstly of its regulator and then of a homologous PspA.
2024-02-15 | PXD044736 | Pride
Project description:The purpose of this study was to use chemical similarity evaluations, transcriptional profiling, in vitro toxicokinetic data and physiologically based pharmacokinetic (PBPK) models to support read across for a series of branched carboxylic acids using valproic acid (VPA), a known developmental toxicant, as a comparator. The chemicals included 2-propylpentanoic acid (VPA), 2-ethylbutanoic acid (EBA), 2-ethylhexanoic acid (EHA), 2-methylnonanoic acid (MNA), 2-hexyldecanoic acid (HDA), 2-propylnonanoic acid (PNA), dipentyl acetic acid (DPA) or 2-pentylheptanoic acid (PHA), octanoic acid (OA, a straight chain alkyl acid) and 2-ethylhexanol. Transcriptomics was evaluated in four cell types (A549, HepG2, MCF7 and iCell cardiomyocytes) 6 hours after exposure to 3 concentrations of the compounds, using the L1000 platform. The transcriptional profiling data indicate that two- or three-carbon alkyl substituents at the alpha position of the carboxylic acid (EHA and PNA) elicit a transcriptional profile similar to the one elicited by VPA. The transcriptional profile is different for the other chemicals tested, which provides support for limiting read across from VPA to much shorter and longer acids. Molecular docking models for histone deacetylases, the putative target of VPA, provides a possible mechanistic explanation for the activity cliff elucidated by transcriptomics. In vitro toxicokinetic data was utilized in a PBPK model to estimate internal dosimetry. The PBPK modeling data show that as the branched chain increases, predicted plasma Cmax decreases. This work demonstrates how transcriptomics and other mode of action-based methods can improve read across.
2024-11-01 | GSE218438 | GEO